$,FileReference-method	FileReference
$<-,FileReference-method	FileReference
BamFileReference	BamFileReference
BamFileReference-class	BamFileReference
BamIndexWrapper	BamFileReference
BamIndexWrapper-class	BamFileReference
BamWrapper	BamFileReference
BamWrapper-class	BamFileReference
BcfFileReference	BcfFileReference
BcfFileReference-class	BcfFileReference
BedFileReference	BedFileReference
BedFileReference-class	BedFileReference
BedWrapper	BedFileReference
BedWrapper-class	BedFileReference
BgzipIndexWrapper	BgzipIndexWrapper
BgzipIndexWrapper-class	BgzipIndexWrapper
BigBedFileReference	BigBedFileReference
BigBedFileReference-class	BigBedFileReference
BigBedWrapper	BigBedFileReference
BigBedWrapper-class	BigBedFileReference
BigWigFileReference	BigWigFileReference
BigWigFileReference-class	BigWigFileReference
BigWigWrapper	BigWigFileReference
BigWigWrapper-class	BigWigFileReference
CompressedIndexedWrapper-class	virtual-wrapper
CompressedWrapper-class	virtual-wrapper
compression	virtual-wrapper
FaIndexWrapper	FastaFileReference
FaIndexWrapper-class	FastaFileReference
FastaFileReference	FastaFileReference
FastaFileReference-class	FastaFileReference
FastaWrapper	FastaFileReference
FastaWrapper-class	FastaFileReference
FastqFileReference	FastqFileReference
FastqFileReference-class	FastqFileReference
FastqWrapper	FastqFileReference
FastqWrapper-class	FastqFileReference
FileReference	FileReference
FileReference-class	FileReference
GffFileReference	GffFileReference
GffFileReference-class	GffFileReference
GffWrapper	GffFileReference
GffWrapper-class	GffFileReference
GmtFileReference	GmtFileReference
GmtFileReference-class	GmtFileReference
GmtWrapper	GmtFileReference
GmtWrapper-class	GmtFileReference
index	virtual-wrapper
index,IndexedWrapper-method	virtual-wrapper
IndexedWrapper-class	virtual-wrapper
loadBamIndexWrapper	BamFileReference
loadBamWrapper	BamFileReference
loadBedWrapper	BedFileReference
loadBgzipIndexWrapper	BgzipIndexWrapper
loadBigBedWrapper	BigBedFileReference
loadBigWigWrapper	BigWigFileReference
loadFaIndexWrapper	FastaFileReference
loadFastaWrapper	FastaFileReference
loadFastqWrapper	FastqFileReference
loadGffWrapper	GffFileReference
loadGmtWrapper	GmtFileReference
loadTabixIndexWrapper	TabixIndexWrapper
loadVcfWrapper	BcfFileReference
path	virtual-wrapper
path,FileReference-method	FileReference
path,Wrapper-method	virtual-wrapper
readBamFileReference	BamFileReference
readBcfFileReference	BcfFileReference
readBedFileReference	BedFileReference
readBigBedFileReference	BigBedFileReference
readBigWigFileReference	BigWigFileReference
readFastaFileReference	FastaFileReference
readFastqFileReference	FastqFileReference
readGffFileReference	GffFileReference
readGmtFileReference	GmtFileReference
saveObject,BamFileReference-method	BamFileReference
saveObject,BcfFileReference-method	BcfFileReference
saveObject,BedFileReference-method	BedFileReference
saveObject,BigBedFileReference-method	BigBedFileReference
saveObject,BigWigFileReference-method	BigWigFileReference
saveObject,FastaFileReference-method	FastaFileReference
saveObject,FastqFileReference-method	FastqFileReference
saveObject,GffFileReference-method	GffFileReference
saveObject,GmtFileReference-method	GmtFileReference
show,CompressedIndexedWrapper-method	virtual-wrapper
show,CompressedWrapper-method	virtual-wrapper
show,FastaWrapper-method	FastaFileReference
show,FastqWrapper-method	FastqFileReference
show,FileReference-method	FileReference
show,IndexedWrapper-method	virtual-wrapper
show,Wrapper-method	virtual-wrapper
stageObject,BamIndexWrapper-method	BamFileReference
stageObject,BamWrapper-method	BamFileReference
stageObject,BedWrapper-method	BedFileReference
stageObject,BgzipIndexWrapper-method	BgzipIndexWrapper
stageObject,BigBedWrapper-method	BigBedFileReference
stageObject,BigWigWrapper-method	BigWigFileReference
stageObject,FaIndexWrapper-method	FastaFileReference
stageObject,FastaWrapper-method	FastaFileReference
stageObject,FastqWrapper-method	FastqFileReference
stageObject,GffWrapper-method	GffFileReference
stageObject,GmtWrapper-method	GmtFileReference
stageObject,TabixIndexWrapper-method	TabixIndexWrapper
stageObject,VcfWrapper-method	BcfFileReference
TabixIndexWrapper	TabixIndexWrapper
TabixIndexWrapper-class	TabixIndexWrapper
VcfWrapper	BcfFileReference
VcfWrapper-class	BcfFileReference
virtual-wrapper	virtual-wrapper
Wrapper-class	virtual-wrapper
[[,FileReference-method	FileReference
[[<-,FileReference-method	FileReference
